Specification Sheet: Genefficiency Copy Number Variation (CNV)

Tuesday 23 August 2011

Applications:: Genomic services

Specifications for Oxford Gene Technology (OGT) microarray service for CNV studies.

Measurable	Enzymatic CNV	ULS CNV
360° QC	DNA QC on sample arrival QC of sample labelling efficiency LIMS sample tracking
Microarray platform	Agilent SurePrint™ HD and G3 CGH microarray
Species covered	Catalogue: Human, mouse, rat, chicken Bespoke: Designed using eArray or the Oligome™; our library of >24 million high resolution CNV probes spanning the entire genome
Array density	1x244k, 2x105k , 4x44k, 8x15k G3: 1x1M, 2x400k, 4x180k, 8x60k	1x244k, 2x105k , 4x44k, 8x15k G3: 1x1M, 2x400k, 4x180k, 8x60k
Experimental design consultancy	Avaliable on request
Sample preparation consultancy	Available on request
Starting sample	Genomic DNA from blood, cells, or frozen tissues	FFPE and genomic DNA from blood, cells, or frozen tissues
Starting sample requirement	260/280 >1.8 260/230 >1.8 1x: 0.5–3.0 μg 2x: 0.5–1.5 μg 4x: 0.5–1.5 μg 8x: 0.2–0.5 μg	260/280 >1.8 260/230 >1.8 1x: 2.0 μg 2x: 1.0 μg 4x: 0.5 μg 8x: 0.25 μg
Sample QC method	NanoDrop™ 8000 spectrophotometer and gel electrophoresis	NanoDrop 8000 spectrophotometer and Agilent Bioanalyzer 2100
Labelling method	Enzymatic labelling	Kreatech ULS
Slide printing	Agilent SurePrint technology
Replicate no. of probes	Tiling array: Variable numbers of multiple single probes per CNV region
Tm equalised	Yes
Database version	Genome build: hg18
Custom sequences	Can be added
Custom design by OGT	Available on request
Single/dual colour	Both
Dynamic range	5 logs
Data analysis	Tailored to customer requirements (includes feature extraction, QC report, CytoSure™ analysis)
Data format	Tailored to customer requirements TIFF images, XML files, TXT files (raw data), customer report, relevant data analysis files (e.g. CytoSure), QC report